Contacts of the strand formed by residues 264 - 268 (chain V) in PDB entry 1UW9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 264 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199V PHE* 4.4 9.6 - - + -
237V GLY* 4.2 9.0 - - - -
238V HIS 3.0 47.0 - - - +
239V TYR* 3.5 36.6 - - + -
240V LEU* 3.3 7.7 + - - +
262V VAL* 3.6 5.5 + - - +
263V PRO* 1.3 82.9 - - + +
265V ILE* 1.3 80.1 + - - +
289V LEU* 4.1 1.5 - - - +
290V PHE* 3.6 29.8 - - + +
291V LEU 4.9 0.2 - - - -
292V HIS* 4.2 8.1 - - + +
325V HIS* 3.9 20.4 - - + +
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Residues in contact with ILE 265 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218V PHE* 5.3 1.3 - - + -
239V TYR* 4.3 2.2 - - - -
240V LEU* 3.2 19.1 - - + +
242V ALA* 4.2 8.7 - - + -
253V ARG 5.1 1.1 - - - +
254V ALA* 3.9 17.3 - - + -
257V ALA* 3.5 32.1 - - + -
264V ILE* 1.3 83.9 - - - +
266V MET* 1.3 63.0 + - - +
280V LEU* 3.9 28.7 - - + -
284V CYS* 3.7 23.8 - - - -
289V LEU* 4.3 8.7 - - + +
290V PHE 3.0 14.6 + - - +
291V LEU* 3.5 6.2 - - + -
292V HIS 2.8 23.2 + - - -
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Residues in contact with MET 266 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201V KCX 3.6 27.1 - - - +
202V ASP* 3.2 25.6 - - - +
204V GLU* 4.0 5.6 - - - -
239V TYR* 3.6 31.6 - - + +
240V LEU 2.9 7.5 + - - -
241V ASN* 3.4 33.5 + - - +
242V ALA* 2.9 29.5 + - - +
265V ILE* 1.3 75.1 - - - +
267V HIS* 1.3 62.6 + - - +
268V ASP* 3.8 16.8 - - - +
280V LEU* 4.6 0.2 - - - +
291V LEU* 4.2 3.6 - - - -
292V HIS* 3.0 16.8 - - + +
294V HIS* 4.0 13.5 - - + -
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Residues in contact with HIS 267 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275O THR* 4.9 2.5 - - - -
243V THR* 3.5 22.9 + - + -
244V ALA 5.3 0.2 - - - -
250V MET* 3.9 18.7 - - - -
266V MET* 1.3 76.4 - - - +
268V ASP* 1.3 78.1 + - - +
269V TYR* 3.3 13.0 + - - -
272V GLY* 4.0 14.6 - - - -
273V GLY 4.0 5.5 + - - -
276V ALA* 4.3 2.2 - - + +
277V ASN* 2.8 55.3 + - + +
280V LEU* 3.6 23.0 - - + +
291V LEU* 4.0 4.7 - - + -
292V HIS 2.9 6.1 + - - -
293V ILE* 3.4 7.5 - - + +
294V HIS* 3.0 22.2 + - - -
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Residues in contact with ASP 268 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118O THR* 3.2 15.2 - - - +
204V GLU* 2.7 34.7 - - - +
243V THR* 2.9 31.2 + - + +
266V MET* 3.8 7.6 - - - +
267V HIS* 1.3 74.3 + - - +
269V TYR* 1.3 57.5 + - - +
270V LEU 3.2 2.6 + - - -
271V THR* 3.1 17.0 - - - +
272V GLY* 2.9 27.7 + - - -
294V HIS* 3.4 28.1 - - - +
296V ALA* 4.5 6.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il